Select the virtual server / domain which you want to enable SSL protocol with SSL certificate from Let’s Encrypt from the drop-down list.

Select Edit Virtual Server.

Go to Enabled Features.

Check the SSL website enabled?. Hit Save Virtual Server when done.

Now go to Server Configuration -> Manage SSL Certificate.

Go to Let’s Encrypt tab.

Under Request certificate for, select the radio button for Domains associated with this server which allows Virtualmin to automatically decide the domains for the SSL certificate (typically the root domain and its www subdomain), or Domain names listed here, where you can list the domain names (one per line) that you want to include in the SSL certificate manually.

Virtualmin also supports auto renewal of Let’s Encrypt certificate. To do so, select the radio button next to the empty textbox for Months between automatic renewal option, then enter a number between 1 to 3 months in the text box.

Hit Request Certificate when done.

Once done, Virtualmin will automatically install SSL certificate and configure the web server to use the new certificate and key. You can now visit your website via HTTPS secure connection, which should automatically trusted by most web browsers, and see it protected with a padlock.